User: ariel.balter

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ariel.balter10
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Posts by ariel.balter

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Benchmark - Comparison of Different NGS Mappers
... Good point @joe.cornish826. The OP used a data presentation style known to be a poor practice in order to show barely perceptible differences in data which is reported as a single number taken from a process that has a random component. They have no way of knowing if the differences are a complete f ...
written 13 days ago by ariel.balter10
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Answer: A: Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak callin
... In my case, I can ask the lab that did the sequencing, and they can tell me EXACTLY what the fragment size distribution is. I would try talking to them. The fragment size reported by the lab that did the PCR is undoubtedly going to be better than any software estimate. ...
written 17 days ago by ariel.balter10
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Answer: A: sicer chip seq analysis
... You might want to look into SICER's new incarnation in [EPIC](https://github.com/biocore-ntnu/epic). You will find it much more accessible. And the creator is very responsive to issues on GitHub and answering questions if they are posted here or on Stackoverflow. ...
written 17 days ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Looks like it is still trying: balter@server:~$ which python /home/.../Applications/miniconda3/bin/python balter@server:~$ python -V Python 3.5.2 balter@server:~$ conda install tophat Fetching package metadata ............. Solving package specifications: .......... ...
written 5 weeks ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Hi @Devon--that's great! Just to clarify: is this for the `tophat` code, the `bowtie2` code, or the conda recpie? ...
written 5 weeks ago by ariel.balter10
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MACS2 coverage calculations
... This relates to https://www.biostars.org/p/232347/ I'm trying to understand the output `macs2 callpeak` gives. As you can see, there are some identical coordinate ranges for which macs gives multiple, different fold changes, p-values, and q-values. However, when I calculate their coverage using `be ...
macs2 chip-seq written 5 weeks ago by ariel.balter10
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MACS2 Narrow peak (narrowPeak) output format
... According to the [macs2 documentation](https://github.com/taoliu/MACS#call-peaks), column 7 of the `*.narrowPeak` output bedfiles is supposed to be the fold change. However, using `bedtools multicov` I get a different result. $ bedtools multicov -bams ../bam/mock_lsd1_A.bam ../bam/mock_input_A. ...
macs2 chip-seq written 5 weeks ago by ariel.balter10 • updated 16 days ago by Biostar ♦♦ 10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... I get the usual I/O error with using python 3 balter@server:...users/balter/tophat/test_data$ conda create --name bowtietest bowtie2=2.2.5 tophat Fetching package metadata ............. Solving package specifications: .......... Package plan for installation in environment .../ ...
written 5 weeks ago by ariel.balter10
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
... Thanks. My group is discussing this right now. I'm actually not the fusion person, but I was trying to get a working `conda` recipe going for them. Turns out to be two things: 1) python 3 incompatibility in conda recipe and 2) bowtie2 + tophat version incompatibility. https://github.com/bioconda/bio ...
written 5 weeks ago by ariel.balter10
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Tophat and Bowtie installed with Conda not working on test data.
... I created a python 2.7 environment using conda, and installed tophat and bowtie. I'm trying the test data as specified here: https://ccb.jhu.edu/software/tophat/tutorial.shtml#inst However, I get the following error: balter@server3:/.../users/balter/tophat/test_data$ source activate p27 ( ...
tophat miniconda anaconda conda bowtie written 5 weeks ago by ariel.balter10

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